Include networkx in ext folder and add to setup.py
Fix bug where color variable went out of scope
Add git back into doc script
Revert "Add git back into doc script"

This reverts commit f3acc546b28e5ec4ad71cf65adf4c0adcc26c09f.
Fix indent typo
Improved git handling
Renamed variable for clarity
Add stash if changes can't be commited
Add objective test case and files
Move ForceBalanceBaseClass and BaseReader to __init__

Since ForceBalanceBaseClass and BaseReader are needed by a number of other
forcebalance classes but don't do anything themselves, they can be moved
to __init__ as forcebalance.BaseClass and forcebalance.BaseReader. This is
more in line with standard python programming practices and consolidates
common classes used across the forcebalance package into one place.
Adjust module imports for consistency
Stop redirecting stdout
print --> logger
convert print to logger
Convert forcefield to logging
Convert target to logging
Convert abinitio to logging
Convert fdwrap to logging
Add logger to finite_difference
Improve KeyboardInterrupt handling